emorycn2l/emory_centiloid repository overview

⁠Emory Centiloid PET Processing Docker

This Docker image provides a pipeline for processing PET images for the Emory Centiloid project.

⁠Authors

• Qixiang Lin, PhD
• Junjie Wu, PhD
• Deqiang Qiu, PhD

⁠Usage

Run the container with your input and output directories mounted:

docker run -v /path/to/input:/input -v /path/to/output:/output emorycn2l/emory_centiloid \
  -tracer pib|av45|florbetapir [-PET PET_FILE] [-T1 T1_FILE] [-help]

Example:

docker run \
       -v "BIDS/sub001:/input" \
       -v "emoryCentiloid/sub001/:/output" \
       emorycn2l/emory_centiloid \
       -tracer pib \
       -PET "/input/pet/sub001_task-rest_trc-pib_pet.nii" \
       -T1 "/input/anat/sub001_T1w.nii"

⁠Options

• -tracer (required): Specify tracer type. Supported values: pib, av45, florbetapir
• -PET: PET image filename (optional, default: PET.nii)
• -T1: T1 image filename (optional, default: T1.nii)
• -help: Show usage help and exit

⁠Input

• Place your PET and T1 images in the /input directory (or specify filenames with -PET and -T1).

⁠Output

• Results and QC images are saved in /output/emory_centiloid/.
• Key results and input parameters are saved in emory_centiloid_output.json.
• QC reports are saved in report.html and report.pdf along with png files

⁠Output JSON Example

{
  "pipeline_name": "Emory_Centiloid",
  "version": "1.0.0",
  "execution_time": "YYYY-MM-DD HH:MM:SS",
  "tracer": "av45",
  "PET_file": "PET.nii",
  "T1_file": "T1.nii",
  "ctx_SUV": "value",
  "ref_SUV": "value",
  "whole_brain_SUVR": "value",
  "centiloid": "value"
}

⁠Notes

• Centiloid is calculated only for tracers av45 and florbetapir.
• The pipeline uses FSL, SPM, and other neuroimaging tools.
• Make sure your input files are named correctly or specify them with the command line options.

⁠License

⁠License for Emory Centiloid Pipeline

This work, including all original code, configuration, and documentation files provided in this repository or Docker image, is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).

You are free to:

• Share — copy and redistribute the material in any medium or format
• Adapt — remix, transform, and build upon the material

Under the following terms:

• Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made.
• NonCommercial — You may not use the material for commercial purposes.

Full license text: https://creativecommons.org/licenses/by-nc/4.0/legalcode⁠
Summary: https://creativecommons.org/licenses/by-nc/4.0/⁠

⁠Preferred Attribution:

If you use this software, please cite:

⁠Third-Party Software and Licenses

This project includes or distributes the following third-party components, each of which is licensed separately and not covered under the CC BY-NC 4.0 license:

1. MATLAB Runtime

   • Provided by: MathWorks
   • License: Redistribution is permitted only for running compiled MATLAB applications.
   • License link: https://www.mathworks.com/help/matlab/matlab_external/install-and-run-matlab-runtime.html⁠
   • Note: You must agree to the MathWorks terms when using MATLAB Runtime.

2. AFNI (Analysis of Functional NeuroImages)

   • Provided by: NIH (NIMH)
   • License: GNU General Public License v2 (GPL-2.0)
   • License link: https://afni.nimh.nih.gov/afni/about/license⁠
   • Source: https://github.com/afni/afni⁠
   • Note: The AFNI components included in the Docker image are unmodified binaries distributed in compliance with the GPL.

3. FSL (FMRIB Software Library)

   • Provided by: University of Oxford
   • License: FSL Software License (custom academic/research use license)
   • License link: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence⁠
   • Note: FSL is free for non-commercial research use only. Commercial use requires a separate license from Oxford University Innovation.

4. SPM Standalone

   • Provided by: Wellcome Centre for Human Neuroimaging, UCL
   • License: SPM Software License (freely available for academic use)
   • License link: https://www.fil.ion.ucl.ac.uk/spm/disclaimer.html⁠
   • Note: Requires MATLAB Runtime. Refer to SPM site for full license details.

5. Centiloid Project VOI Definitions

   • Source: The Centiloid Project, https://www.gaain.org/centiloid-project⁠
   • Description: Standardized VOI (Volume of Interest) masks for amyloid PET quantification
   • Attribution: Derived from materials developed by the Centiloid Working Group
   • License: The Centiloid Project materials are provided for non-commercial research use only. Redistribution or commercial use may require separate permission from the original developers.

6. CenTauR VOI Definitions

   • Source: CenTauR Project (CenTauR Working Group)
   • Description: Standardized VOI masks and definitions for tau PET quantification
   • Attribution: Derived from materials developed by the CenTauR Working Group
   • License: CenTauR materials are provided for non-commercial research use only. Redistribution or commercial use may require separate permission from the original developers. Refer to the official CenTauR project documentation or repository for full license and usage details.

⁠Redistribution Notice

You may redistribute this Docker image or derivative works only for non-commercial purposes and only if you include:

• This full LICENSE file
• A clear description of which components are covered under which licenses
• All third-party license files and links as required

You are responsible for ensuring compliance with all applicable licenses when using or distributing this image.

⁠For Commercial Use

Commercial use of this software or any modified version is prohibited without prior written permission from the author.

For inquiries, contact: [email protected]⁠